Flurescent marker

ABSTRACT

The invention relates to cyanine dyes, which have alkyl substituents in the meso position of the methine chain, sulphoaryl groups as well as at least one reactive group which permits the binding to a target substance.

[0001] The invention relates to cyanine dyes for use as fluorescent markers.

[0002] Fluorescent dyes are used as markers in many different ways for the analysis of a major part of clinically, biologically, biochemically or chemically relevant substances, such as for example cells, antibodies, proteins, hormones, nucleic acids, oligonucleotides, carbohydrates or amines and mercaptanes. In combination with the easily detectable fluorescence induced by laser (LIF; Laser-Induced Fluorescence), rapid analyses are possible in the aforementioned areas.

[0003] By means of covalent bonding, a larger number of dye molecules are able to be attached to a specimen than is possible in the case of a non-specific non-covalent bond, so that the intensity of the fluorescent light signal is stronger. Furthermore, a covalent bond enables unequivocal marking of a specific target structure in a mixture. For covalent bonding of the fluorescent dye to the specimen, therefore, the dyes are provided with reactive groups. Suitable reactive groups are, for example, the iodacetamid group, the isothiocyanate group, N-succinimide-esters of alkyl carboxylic acids or phosophoramidites of hydroxy alkyl groups.

[0004] In the case of antibodies, proteins, hormones, nucleic acids and other biomolecules, mercapto (—SH), amino (—NH₂) and hydroxy groups (—OH), among others, are available.

[0005] Cyanine dyes are increasingly being used as fluorescent markers. Generally, however, cyanine dyes in solution and at surfaces tend to form aggregates [SCHEIBE: Angew. Chem. 49 (1936) 563; JELLEY: Nature 138 (1936) 1009]. These polymeric dye systems, in contrast with the individual molecule, exhibit a markedly changed absorption and fluorescence behaviour.

[0006] As a result of the aggregation, the absorption maximum may be shifted in comparison with the monomer hypsochrome (Dimers, H-aggregates) or bathochrome (J-aggregates) [DIETZE: J. Signal AM. 1 (1973) 157]. This different absorption behaviour depends on the different dislocation angle between the molecule and aggregate axis as well as the intermolecular spacing of the dyes molecules in the aggregate (packing density). Independently of these influencing variables, it was found that at least seven dye molecules are needed for the formation of J-aggregates [DALTROZZO et al.: Photogr. Sci. Eng. 20 (1974) 441], i.e. J-aggregates are only able to form with raised packing density.

[0007] It is important when using cyanine dyes as fluorescent markers in aqueous systems to prevent the formation of dye aggregates, which fluoresce much more poorly. In addition, there is the fact that the tendency towards increased dye aggregation is accompanied by an increased tendency towards non-specific interactions of the dye at an arbitrary biomolecule.

[0008] Aryl sulpho groups lead to a marked improvement in the water solubility of a dye and should at the same time prevent the formation of dimers or H-aggregates. Corresponding fluorescent markers are described in DE 3.912.046, US 5.268.486 and [MUJUMDAR et al.: Bioconjugate Chem. 4 (1993) 105].

[0009] Using the example of the dye with the following structure

[0010] it could be shown that J-aggregates form in aqueous solution, whereas coupled with proteins, a very marked dimer band could be detected [MUJUMDAR et al.: Bioconjugate Chem. 7 (1996) 356], as a result of which a considerable fluorescence quenching occurs. It goes on to describe how the dimer formation is suppressed by the introduction of two further sulpho groups.

[0011] It has been shown, however, that the fluorescence quantum yield of the protein conjugates both of dye 1 and also 3 decreases by around ¼ compared with free, unconjugated dyes [MUJUMDAR et al.: Bioconjugate Chem. 7 (1996) 356; Terpetschnig: NATO Advanced Research Workshop, Conference Paper, Trieste, 1997].

[0012] The object of the invention is to provide new cyanine dyes which do not exhibit the aforementioned drawbacks and which in particular exhibit a low tendency towards aggregation both in solution as well as on the target molecule and are suitable for application as fluorescent markers in the range from 500 to 700 nm.

[0013] This object is solved by a cyanine dye with the features according to claim 1. Advantageous embodiments and applications emerge from the dependent claims.

[0014] The present invention is illustrated with reference to the figure.

[0015]FIG. 1 shows the VIS spectra of the cyanine dye according to the invention from example 1 in comparison with a known cyanine dye.

[0016] Surprisingly, it was found that, by a new combination of sulphoaryl substituents with alkyl substituents in the meso position of the methine chain, the known drawbacks of the formation of various dye aggregates in solution and also after binding to a target molecule can be eliminated. A cyanine dye according to the invention is distinguished by a combination of sulphoaryl substituents, an alkyl substituent in the meso position of the methine chain and at least one reactive group which permits the binding to target molecule.

[0017] The novel cyanine dyes can be employed with the use of various excitation light sources in the absorption range between 500 and 700 nm and, compared with conventional fluorescent dyes, possess a markedly reduced tendency to aggregation in solution and after binding to a target molecule, e.g. protein.

[0018] Preferred cyanine dyes exhibit the following formulas:

[0019] wherein n=1, 2; R₁ CH₃, C₂H₅; R₂, R₃=H, SO₃M, the four CH groups required to complete a benzene ring, or the four CH groups required to complete a benzene ring including (SO₃M) n; M=H, Na, K.

[0020] In the general formulas 1 to 4, R₄ and R₅ stand for an alkyl group, a sulphoalkyl group, a carboxyl group or a hydroxyl alkyl group (e.g. R₄=(CH₂)_(k)CH₃ with k=0 to 3, (CH₂)_(m)SO₃, (CH₂)_(m)COOH, (CH₂)_(m)CH₂OH, m=2 to 5; R₅=(CH₂)_(m)COOH, (CH₂) _(m)CH₂OH, m=2 to 5).

[0021] In dyes with carboxyl groups, the latter can be converted into their N-succinimide-esters, which then react directly with amino groups on the biomolecule or via a so-called amino linker with hydroxy groups. In dyes with alkyl hydroxy groups, the latter can be converted into phosphoramidites, which react directly with the free 5′-hydroxy group of nucleotides to form a phosphite bond, which subsequently oxidises to form a stable phosphate bond.

[0022] It can be seen from FIG. 1 that the cyanine dyes according to the invention exhibit far better fluorescence properties in the protein conjugate than the conventional cyanine dyes. FIG. 1 shows the VIS spectra of the dye from example 1 [A] and Cy-5 [Amersham) [B] in a comparison after coupling to a protein. As can readily be deduced from the spectra, cyanine dye A according to the invention displays the typical curve shape for a monomer, whereas the development of a dimer band can clearly be recognised in the case of conventional cyanine dye B. Biomolecules can thus be readily marked with the cyanine dyes according to the invention in a perfectly satisfactory fluorescence yield.

EXAMPLES OF EMBODIMENT Example 1

[0023]

[0024] A) Sodium Salt of 1-(5-carboxypentyl)-2,3,3-trimethyl-5-sulphoindolium Bromide:

[0025] 2.61 g of sodium salt of 2,3,3-trimethyl-5-sulpho-indolenine and 2.1 g of 6-bromocaproic acid are caused to react in substance for 2 h at a bath temperature of 110° C. while stirring. After the reaction is completed, acetone is added repeatedly to the oily residue until a solid remains. Yield: 3.4 g.

[0026] B) 1-(5-carboxypentyl)-2-[5-(l-(5-carboxypentyl)-1,3-dihydro-3,3-dimethyl-5-sulpho-2H-indole-2-ylidene)-3-methylpenta-1,3-dienyl]-3,3-dimethyl-5-sulpho-3H-indolium-inner Salt, Sodium Salt:

[0027] 2.3 g of quaternary salt from A) and 0.68 g of 2-methyl-malondianil-hydrochloride are heated in 15 ml of ethanol in the presence of 1 ml each of acetic anhydride and triethylamine for 25 minutes under reflux. After cooling, 2 ml of 3 molar HCl is added and the dye is then precipitated by the addition of ether. (λ=647 nm)

Example 2

[0028]

[0029] Substance A) is produced in the same way as in example 1.

[0030] B) 2-(4-acetaniline-1,3-butadienyl-3-methyl)-3,3-dimethyl-1-ethyl-5-sulphoindolium Hydroxide, Inner Salt:

[0031] 26.7 g of 1-ethyl-2,3,3-trimethyl-5-sulphoindolium hydroxide and 27.3 g of 2-methylmalondianil-hydrochloride are caused to react in 80 ml of acetic anhydride for 1 h at an oil bath temperature of 120° C. After cooling, 600 ml of ethyl acetate is added and drawing off by suction carried out. Yield: 39.6 g.

[0032] C) 1-(5-carboxypentyl)-2-[5-(1,3-dihydro-1-ethyl-3,3-dimethyl-5-sulpho-2H-indole-2-ylidene)-3-methylpenta-1,3-dienyl]-3,3-dimethy-5-sulpho-3H-indolium Hydroxide, Inner Salt, Sodium Salt:

[0033] 2.3 g of the compound from A) and 2.2 g of the compound from B) are dissolved in 20 ml of ethanol and, after the addition of 2 ml triethylamine, heated for 20 minutes under reflux. After the reaction is completed, the mixture is cooled to room temperature, precipitated with ether and the precipitate filtered off. The residue is mixed by stirring with acetone, filtered, absorbed in methanol and a drop of semi-concentrated HCl added. The crude dye obtained after adding diethylether is purified by means of column chromatography over silica gel. (λ=645 nm)

Example 3

[0034]

[0035] Substance A) is produced in the same way as in example 1.

[0036] B) 1-(5-carboxypentyl)-2-[3-(1,3-dihydro-1-(5-carboxypentyl)-3,3-dimethyl-5-sulpho-2H-indole-2-ylidene)-3-methylprop-1-enyl]-3,3-dimethyl-5-sulpho-3H-indolium Hydroxide, Inner Salt, Sodium Salt:

[0037] 2.3 g of quaternary salt from A) and 2.4 g of orthoethyl acetate are heated in 15 ml of pyridine in the presence of 1 ml each of acetic anhydride and triethylamine for 30 minutes under reflux. After cooling, 3 molar HCl is added, the dye is then precipitated with the addition of acetone and boiled off repeatedly with isopropanol. (λ=548 nm)

Example 4

[0038]

[0039] Substance A) is produced in the same way as in example 1.

[0040] B) 1-(5-carboxypentyl)-2-[3-(1,3-dihydro-1-(5-carboxypentyl)-3,3-dimethyl-5-sulpho-2H-indole-2-ylidene)-3-ethylprop-1-enyl]-3,3-dimethyl-5-sulpho-3H-indolium Hydroxide, Inner Salt, Sodium Salt:

[0041] 2.3 g of quaternary salt from A) and 2.7 g of orthopropionic acid triethyl ester are heated in 15 ml of pyridine in the presence of 1 ml each of acetic anhydride and triethylamine for 30 minutes under reflux. After cooling, 3 molar HCl is added, the dye is then precipitated with the addition of acetone and boiled off repeatedly with isopropanol. (λ=549 nm).

Example 5

[0042]

[0043] Substance A) is produced in the same way as in example 1.

[0044] B) Disodium salt of 3-ethyl-6,8-disulpho-1,1,2-trimethyl-benzo[e]-indolium-ethyl-sulphate:

[0045] 4.13 g of disodium salt of 6,8-disulpho-1,1,2-trimethyl-benzo[e]-indolenine and 1.7 g of diethylsulphate are heated in 10 ml of chlorobenzene for 2 h at a bath temperature of 105° C. while stirring. After cooling to room temperature, the chlorobenzene is decanted off. The remaining residue is spread by rubbing repeatedly with acetone. Yield: 4.3 g.

[0046] C) 2-(4-acetaniline-1,3-butadienyl-3-ethyl)-1,1-dimethyl-3-ethyl-6,8-disulpho-benzo[e]-indolium Hydroxide, Sodium Salt:

[0047] 28.3 g of disodium salt of 3-ethyl-6,8-disulpho-1,1,2-trimethyl-benzo[e]-indolium-ethyl-sulphate and 13.7 g of 2-methylmalondianil-hydrochloride are caused to react in 75 ml of acetic anhydride for 1 h at an oil bath temperature of 120° C. After cooling, 550 ml of ethyl acetate is added and drawing off by suction carried out. Yield: 23.5 g

[0048] D) 2-[5-(l-(5-carboxypentyl)-1,3-dihydro-3,3-dimethyl-5-sulpho-2H-indole-2-ylidene)-3-ethyl-penta-1,3-dienyl]-1,1-dimethyl-3-ethyl-6,8-disulpho-1H-benzo[e]indolium-inner salt, disodium salt:

[0049] 2.3 g of the compound from A) and 3.1 g of the compound from B) are dissolved in 15 ml of methanol and, after the addition of 3 ml of triethylamine, heated for 20 minutes under reflux. After cooling to room temperature, precipitation is carried out with diethyl ether. The residue is absorbed in methanol, mixed with 4 ml of acetic acid and precipitated with the addition of ether. The crude dye thus obtained is purified by column chromatography over silica gel. (λ=669 nm). 

1. A cyanine dye, with a combination of sulphoaryl groups, alkyl substituents in the meso position of the methine chain and at least one reactive group which permits binding to biomolecules.
 2. The cyanine dye according to claim 1, characterised by the general structures

wherein n is 1 or 2, R₁ is CH₃ or C₂H₅, R₂ and R₃ are H, SO₃M or the four CH groups required to complete a benzene ring or the four CH groups required to complete a benzene ring including (SO₃M)_(n), whereby M is H, Na or K, and R₄ and R₅ denote equally or differently from another alkyl with 1 to 4 carbon atoms, sulpho alkyl with 2 to 4 carbon atoms, carbox yalkyl with 2 to 6 carbon atoms or hydroxy alkyl with to 6 carbon atoms.
 3. The cyanine dye according to claim 2, characterised in that R₄ and R₅ denote an N-hydroxysuccinimide-ester of e carboxy group (CH₂)_(m)COOH, wherein m is 2 to 5, and a bis-(N,N-di-isopropyl)-β-cyanoethyl-phosphoramidite of the hydroxy group (CH₂)_(m)CH₂OH, wherein m=2 to
 5. 